rs768085739
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM4BP6
The NM_021008.4(DEAF1):c.56_82del(p.Val19_Ala27del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000207 in 1,140,816 control chromosomes in the GnomAD database, including 23 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00019 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00021 ( 23 hom. )
Consequence
DEAF1
NM_021008.4 inframe_deletion
NM_021008.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.45
Genes affected
DEAF1 (HGNC:14677): (DEAF1 transcription factor) This gene encodes a zinc finger domain-containing protein that functions as a regulator of transcription. The encoded proteins binds to its own promoter as well as to that of several target genes. Activity of this protein is important in the regulation of embryonic development. Mutations in this gene have been found in individuals with autosomal dominant cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
EPS8L2 (HGNC:21296): (EPS8 signaling adaptor L2) This gene encodes a member of the EPS8 gene family. The encoded protein, like other members of the family, is thought to link growth factor stimulation to actin organization, generating functional redundancy in the pathways that regulate actin cytoskeletal remodeling. [provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_021008.4.
BP6
?
Variant 11-694965-GCCGCCGCCACAGCGGCCGCGGCCGCCA-G is Benign according to our data. Variant chr11-694965-GCCGCCGCCACAGCGGCCGCGGCCGCCA-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 434934.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=2}.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DEAF1 | NM_021008.4 | c.56_82del | p.Val19_Ala27del | inframe_deletion | 1/12 | ENST00000382409.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DEAF1 | ENST00000382409.4 | c.56_82del | p.Val19_Ala27del | inframe_deletion | 1/12 | 1 | NM_021008.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000190 AC: 28AN: 147146Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000371 AC: 11AN: 29622Hom.: 1 AF XY: 0.000362 AC XY: 7AN XY: 19338
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GnomAD4 exome AF: 0.000209 AC: 208AN: 993560Hom.: 23 AF XY: 0.000220 AC XY: 105AN XY: 477822
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:2Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 19, 2021 | This variant, c.56_82del, results in the deletion of 9 amino acid(s) of the DEAF1 protein (p.Val19_Ala27del), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has not been reported in the literature in individuals with DEAF1-related conditions. ClinVar contains an entry for this variant (Variation ID: 434934). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | DEAF1: BP3 - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 30, 2015 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at